Here are some example R code for the analyses and visualizations in "Modeling and presentation of vaccination coverage estimates using data from household surveys" by Dong and Wakefield (2021) (https://doi.org/10.1016/j.vaccine.2021.03.007).
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data_cleaning.R: code for data cleaning.
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model_fit.R: code for fitting varous models using INLA in R.
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model_prediction.R: code for obtaining posterior prediction samples.
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plot_prediction.R: code for plotting maps of posterior medians and CI width.
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plot_ridgeline.R: code for creating ridgeline plots of posterior distributions.
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plot_rank.R: code for creating histograms of posterior ranking distributions.
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plot_exceedance.R: code for creating maps of posterior exceedence probabilities.
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plot_hatch.R: code for creating state maps with hatching based on coefficient of variation (CV) of vaccination odds.
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model_TCP_quantile.R: code for obtaining quantile intervals, color assignment and true classfication rate (TCP) based on posterior samples.
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plot_TCP_quantile.R: code for plotting maps and histograms with discrete color scales using quantile intervals.
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model_TCP_threshold.R: code for obtaining color assignment and true classfication rate (TCP) given a set of pre-specified intervals based on posterior samples.
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plot_TCP_threshold.R: code for plotting maps and histograms with discrete color scales using a set of pre-specified intervals.